#ifndef __GETOPT__
#define __GETOPT__

#include "getopt.h"

class CommandParser{
public:
	// specify mode: physical or marker or gene based
	char* modevalue;
	// specify map file
	char* mapvalue;
	// specify window size (in bp for physical, in marker count for marker)
	char* windowvalue;
	// specify step size (in bp for physical, in marker count for marker)
	char* stepvalue;
	// specify the refgene file in BED format
	char* genelistvalue;

	CommandParser(int argc, char* argv[]);

};

#endif